Tuesday, May 5, 2020

On The Origin of the Genes of Viruses - 14

An informed public is the purpose of the Dredd Blog grey/gray literature which has appeared here now for over a decade.

Concerning viruses in general, I alluded to the uninformed public recently (if Cosmology is ...).

What would you think of a detective and/or prosecutorial team that had accused a person of being a mass murderer (without really knowing much of the background of the accused)?

For example, if they did not know the parents, the country of origin, the employer, the habits, the maker of the wheelchair the accused uses, or the whereabouts of the accused?

Would that perk up your interest and/or raise your eyebrows?

What if they used, relating to every shred of evidence alleged, the words "it seems", "it could be", "it suggests", "probably", and "we think" to describe their case (a case requiring PROOF beyond a reasonable doubt)?

Shouldn't a mass murdering event which is killing tens and tens of thousands of citizens from every walk of life require proof beyond a reasonable doubt?

Let's consider some questions a serious and competent detective would ask in order to detect the nature of  a suspect.

As to a suspect virus, can it reproduce/replicate itself:
"As viruses are obligate intracellular pathogens they cannot replicate without the machinery and metabolism of a host cell. Although the replicative life cycle of viruses differs greatly between species and category of virus, there are six basic stages that are essential for [pathogenic] viral replication."
(British Socienty for Immunology, emphasis added). Non-pathogenic mutualistic viruses are already inside cells, and do not need to invade because they help the host microbe stay alive and are therefore welcome.

So, would you want to know what the host cell is (its genome etc.)?

A host is like a "family" that brings a biological or viral entity into existence and keeps it from ceasing to exist  (in the sense that if a virus can't replicate/reproduce, then it will die out and become extinct without a host).

The reality about that aspect of viruses is that the relevant prevention science is lame or infantile in several ways, like incompetent detectives in the movie (The Usual Suspects) who had Kaiser in their office without ever knowing anything relevant about him.

So, with that in mind let me ask you when and where have you heard about THE HOST to the corona-virus / Covid-19 in the current media viral 24/7 storm?

I will just say that I have not heard the host even mentioned, and I have heard that viruses can't replicate themselves mentioned only once.

I have, however, heard in the media that viruses can replicate themselves (wrong).

Since most viruses inhabit microbes in a mutualistic relationship, which is beneficial, and since the host is much, much larger than its symbiont virus, why not look for the easier to find host?

I focus on the host, because the last thing a sane society wants to do is change the nature of a mutualitic virus into a pathogen by using antibodies that kill the host (BTW, a host that is helping the human species stay alive - see video below).

If you want to know a lot more about the issue, there are several Dredd Blog series that get deeply into the relevant science involved.

I. Before

When I wrote the previous post in this series about five years ago, I did not exactly envision that the news media would be talking about viruses 24/7 five years later.

Nor did I exactly envision one virus type killing more Americans than had died in the long Vietnam war.

But, I can say that I have covered the issues concerning the origin of viruses by contemplating their genetic characteristics and those of their hosts (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13; The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11; etc. see the series tabs at the top of the page).

II. During

During the contemplation of the genes of viruses, uncertainty arose as a scientific principle or reality as the case may be.

Something caught my attention:
I kept thinking about the implications until it dawned on me that one aspect of the uncertain gene concept, elucidated upon in this series, is that proton tunnelling is also technically "epigenetic."

I mean that in the sense that any gene itself, in all genetic circumstances, does not "control" itself or anything else.

Thus Epigenetics, a discipline in and of itself, is a realm that studies what utilizes the genetic molecules, where those genetic molecules are utilized, when those molecules are utilized, how they are utilized, and why those molecules are utilized.
(The Uncertain Gene - 11). I went on to write:
... the nomenclature of Epigenetics covers all activity that acts upon gene molecules, including those that decide whether, for example, to turn the gene on or off:
Geneticists study the gene; however, for epigeneticists, there is no obvious 'epigene'. Nevertheless, during the past year, more than 2,500 articles, numerous scientific meetings and a new journal were devoted to the subject of epigenetics. It encompasses some of the most exciting contemporary biology and is portrayed by the popular press as a revolutionary new science — an antidote to the idea that we are hard-wired by our genes. So what is epigenetics? - (Perceptions of Epigenetics)

Much work has been published on the cis-regulatory elements that affect gene function locally, as well as on the biochemistry of the transcription factors and chromatin- and histone-modifying complexes that influence gene expression. However, surprisingly little information is available about how these components are organized within the three-dimensional space of the nucleus. Technological advances are now helping to identify the spatial relationships and interactions of genes and regulatory elements in the nucleus and are revealing an unexpectedly extensive network of communication within and between chromosomes [cf. this]. A crucial unresolved issue is the extent to which this organization affects gene function, rather than just reflecting it. - (Nuclear organization of the genome and the potential for gene regulation)

(see following link for more ...)
(Nature Insight: Epigenetics, Vol. 447, No. 7143 pp 396-440). The point is that epigenetic dynamics involve multiple levels of analysis and subsequent operations ...
(ibid). The issue of Epigenetics (epi means above) informs us that in order to understand viruses we must have a handle on, an understanding of, their hosts.


Contrary to some media programs on TV, viruses do not replicate or reproduce, instead they are replicated or reproduced by machinery inside their host.

I am talking about a vast array machinery ("Ribosome: a sophisticated molecular machine") that is not part of any virus ... machinery that is part of the host microbe.

Even more interesting perhaps is that most viruses are mutualists, meaning that they do something helpful ("If not for a virus, none of us would ever be born") to their host (only a minority of viruses, the pathogenic viruses are harmful).

Why do they go crazy when their host is killed by chemicals and other antibiotics produced in the civilized world that is "at war" with the microbial world?

That is the same as asking "what causes viral diseases?"

III. After

Can you say "situation ethics" ...
"Small studies that build on basic science and preclinical research in early phases of drug development routinely generate signals of promise that are not confirmed in subsequent trials. Even when new drugs are established to be safe and effective, rarely are their benefits so massive that they can be detected in small, open-label, nonrandomized trials. The proliferation of small studies that are not part of an orchestrated trajectory of development is a recipe for generating false leads that threaten to divert already scarce resources toward ineffective practices, slow the uptake of effective interventions because of an inability to reliably detect smaller but clinically meaningful benefits, and engender treatment preferences that make patients and clinicians reluctant to participate in randomized trials. These problems are amplified by published reports of compassionate use, which was designed as an alternative pathway to access interventions outside of research, not to support systematic evaluation."
(Against pandemic research exceptionalism). Can you say "knee jerk reaction"?

Can you say "the traditional yellow peril" from Wuhan is quite erroneously the usual suspect?

Even as (what should be suspects) U.S. meat packing plants and other animal torture sites rack up the highest per capita covid-19 cases (places where the greatest overuse of antibiotics is centered)?

The possibility that virus pandemics can spring and spread from many origins is only as secret as Big Meat and Big Pharma want it to be:
"In addition, the meat and food industry are vulnerable to a variety of other infectious diseases that can manifest in food processing areas due mainly to poor personal hygiene and processing sanitation practices, which in turn can develop the growth of bacteria, viruses, moulds, and yeasts. These can then set the stage for:

Foodborne infection, such as salmonella or trichinosis, caused by ingesting food that is contaminated with bacteria, parasites, and viruses

Foodborne intoxication, either bacterial, such as E. coli, or chemical, where food has been contaminated with toxic chemicals, such as cleaning compounds or pesticides"
(Meat Cutting and Processing for Food Service, emphasis added; cf. Trump Policy Maximizes Deaths in Food Factories). Don't forget that helpful bacteria are hosts to helpful viruses.

Scientists speak of both a pathogenic and a non-pathogenic corona virus (COVID-19 coronavirus epidemic has a natural origin) without discussing the microbial host (bats and camels are not microbes) or the circumstances that would change a non-pathogenic to a pathogenic virus.

Viruses can become pathogenic when a catastrophe (e.g. antibiotic killing) happens to their host (What Did The Mass Extinctions Do To Viruses and Microbes?).

IV. Closing Comments

Because we may be entering a new age of viral epidemics and pandemics, I am reopening this series that has been dormant for several years.

I am doing so in order to see if we can find the microbe that is being mass-murdered and thereby rendering the covid-19 virus host-less (homeless) like the boll weevil ... looking for a host (High Technology Boll Weevil).

The next post in this series is here, the previous post in this series is here.

The genetic material of a human is >90% microbial ... (lots of host homes for lots of viruses) ...

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